Peaky maps physical contacts between different regions of DNA by recognizing peaks in a Capture Hi-C (CHi-C) signal for a specific region of interest. It accounts for technical and biological noise, and subsequently finds regions around which the residual signal peaks and then decays with distance. The algorithm finds sets of regions at which peaks of varying strengths combinedly explain the normalized CHi-C signal. The probability of these regions contacting a region of interest is then quantified.
The following R commands should install the package:
install.packages("devtools")
library(devtools)
install_github("cqgd/R2BGLiMS")
install_github("cqgd/pky")
The (modified) R2BGLiMS package requires a Java JDK (alternative: OpenJDK) to function.
On a fresh installation of Ubuntu, the dependencies also require libssl-dev and libcurl4-openssl-dev, installed via:
sudo apt-get update
sudo apt-get install libssl-dev libcurl4-openssl-dev
To finemap interactions from scratch, starting with interaction counts (N between fragment A and B), see the standard workflow tutorial. To finemap interactions previously called by CHiCAGO, try the example code for CHiCAGO-based analyses here.